Can CLC genomics read mapping files be used in Bioconductor/R and HTSeq-counts?

[tdelaney]

I have been using CLC Genomics for RNA-seq analyses. I am using the gaussian-based tests in CLC Genomics to detect differentially expressed genes but I am interested in using Bioconductor/R packages, such as DESeq. Can I use the exported bam/sam files produced from CLC's RNA-seq mapping tool in DESeq? Or do I need to use bam/sam files from another mapper such as TopHat? Additionally, can I use the bam/sam files from CLC as input into the HTSeq-count program? Thank in advance for you help.

[Jeremy]

You can use a sorted bam file as input for HTSeq-count (assuming CLC generates a regular bam file) to get read counts per sample and then merge these into a table of read counts per gene (rows) for each sample (columns) as input for DESeq.